Colour intensity and retention are key quality traits for most fruits and vegetables as well as some cereals such as maize kernels and more recently "Golden Rice". In the case of hot pepper, (Capsicum), products if fruit colour degrades or does not reach a specified intensity the breeder and primary producer will not obtain adequate financial return and the crop will be rendered worthless. Thus, there is great interest and commercial incentives for seeds (hybrids) having robust colour retaining phenotypes. Through previous iCASE funding between the applicants and the internal Syngenta programme, the applicants have (i) identified carotenoids as the molecules conferring colour intensity, (ii) implemented an image analysis method for the rapid determination of colour intensity and retention in the field, (iii) created a discovery population segregating for colour retention (iv) shown that colour intensity and retention are two separate traits and (v) identified gene specific candidates for colour intensity and potential molecular and biochemical components responsible for colour retention. The latter includes differential levels and isoform abundance of Super Oxide Dismutase (SOD) and Catalase (CAT) enzymes which, through the analysis of volatile components, appear to initiate pigment degradation via lipid peroxidation. This would appear to be a similar mechanism to the post-harvest deterioration experienced in Cassava tuber (Jia, et al. 2013. Plant Physiol. 161, 1517), which demonstrates the generic cross crop importance of the phenomena. In the present proposal it is intended to first focus on several accessions that display tolerance and susceptibility to colour retention and use modern metabolomics and transcriptomics to identify processes and candidates involved in colour retention. Concurrently, more focused biochemical studies will be carried out on SOD and CAT activities in these lines along with the analysis of lipid peroxidation species and their interaction with carotenoids. Subsequently fixed discovery populations prepared with control lines and genotypes displaying colour retention will be screened for colour retention properties. In a sub-population showing differential colour retention phenotypes metabolomics and transcriptomics will be performed and the co-localisation of molecular and biochemical candidates to colour retention elucidated in order to identify genomic regions conferring colour retention traits. This programme of activities is synergistic to the long-term funded activities and aspirations of the academic and non-academic partners. The proposed experimental programme will provide the student with the opportunity to gain expertise in modern "omic" based technologies and traditional biochemical studies in an applied /translational context.